Wenhao Tang
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/bayNorm |
| git_branch: RELEASE_3_16 |
| git_last_commit: 7bd8b14 |
| git_last_commit_date: 2023-01-19 11:15:02 -0400 (Thu, 19 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:04:58 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the bayNorm package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bayNorm.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 127/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bayNorm 1.16.2 (landing page) Wenhao Tang
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: bayNorm |
| Version: 1.16.2 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings bayNorm_1.16.2.tar.gz |
| StartedAt: 2023-04-10 19:09:34 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:12:20 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 165.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bayNorm.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:bayNorm.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings bayNorm_1.16.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/bayNorm.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘bayNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bayNorm’ version ‘1.16.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bayNorm’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
libs 5.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘bayNorm.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/bayNorm.Rcheck/00check.log’
for details.
bayNorm.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL bayNorm
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘bayNorm’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c bayNorm_main.cpp -o bayNorm_main.o
bayNorm_main.cpp: In function ‘Rcpp::List EstPrior_sprcpp(arma::sp_mat)’:
bayNorm_main.cpp:1374:7: warning: variable ‘Nrows’ set but not used [-Wunused-but-set-variable]
1374 | int Nrows;
| ^~~~~
bayNorm_main.cpp: In function ‘Rcpp::List EstPrior_rcpp(Rcpp::NumericMatrix)’:
bayNorm_main.cpp:1427:7: warning: variable ‘Nrows’ set but not used [-Wunused-but-set-variable]
1427 | int Nrows;
| ^~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o bayNorm.so RcppExports.o bayNorm_main.o -fopenmp -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-bayNorm/00new/bayNorm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bayNorm)
bayNorm.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(bayNorm)
>
> test_check("bayNorm")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
6.724 0.412 7.123
bayNorm.Rcheck/bayNorm-Ex.timings
| name | user | system | elapsed | |
| AdjustSIZE_fun | 0.004 | 0.004 | 0.008 | |
| BB_Fun | 0.071 | 0.012 | 0.084 | |
| BetaFun | 0.013 | 0.000 | 0.014 | |
| Check_input | 0.008 | 0.000 | 0.008 | |
| DownSampling | 0.002 | 0.000 | 0.002 | |
| EXAMPLE_DATA_list | 0.002 | 0.000 | 0.002 | |
| EstPrior | 0.003 | 0.000 | 0.003 | |
| EstPrior_rcpp | 0.001 | 0.000 | 0.001 | |
| EstPrior_sprcpp | 0.002 | 0.000 | 0.002 | |
| NOISY_FUN | 0.140 | 0.008 | 0.148 | |
| Prior_fun | 0.042 | 0.003 | 0.045 | |
| SyntheticControl | 0.004 | 0.001 | 0.005 | |
| asMatrix | 0.001 | 0.000 | 0.001 | |
| as_matrix | 0.001 | 0.000 | 0.002 | |
| bayNorm | 0.049 | 0.000 | 0.049 | |
| bayNorm_sup | 0.047 | 0.000 | 0.048 | |
| noisy_gene_detection | 0.09 | 0.00 | 0.09 | |
| t_sp | 0.001 | 0.000 | 0.001 | |